Sniffles is a structural variation (SV) caller using third-generation sequencing data such as those from Pacific Biosciences or Oxford Nanopore platforms. It detects all types of SVs using evidence from split-read alignments, high-mismatch regions, and coverage analysis.

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This panim wrapper for Heng Li’s kexpr math expression library.

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This package provides development tools for developing applications of the NCARG command library, such as wrappers for compilation of NCL executables.

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Entrez Direct (EDirect) is an advanced method for accessing NCBI’s set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a terminal window or script. Functions take search terms from command-line arguments. Individual operations are combined to build multi-step …

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Simka is a de novo comparative metagenomics tool. Simka represents each dataset as a k-mer spectrum and compute several classical ecological distances between them.

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MetaBAT integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency for accurate metagenome binning. MetaBAT outperforms alternative methods in accuracy and computational efficiency on both synthetic and real metagenome datasets. It automatically forms hundreds of high quality genome …

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